1 MA plots

1.1 Fold-change cutoff 2

Cold v Ctrl MA plot

Hot v Ctrl MA plot

1.2 No fold-change cutoff

Cold v Ctrl MA plot

Hot v Ctrl MA plot

1.3 No fold-change cutoff (fdr < 0.01)

Cold v Ctrl MA plot

Hot v Ctrl MA plot

2 Top 50 differentially expressed genes by padj

2.1 Heat shock

gene hot_fc log2FoldChange.hot padj.hot
CG3339 down -5.155 1.097e-27
l(2)08717 down -2.3 4.051e-25
pip down -3.434 5.188e-24
stan down -2.592 2.063e-23
Dhc36C down -2.724 1.51e-22
ft down -3.361 4.602e-22
CG17075 down -2.455 5.379e-22
CG1801 down -3.692 2.458e-21
CG9492 down -4.122 2.881e-20
Dhc93AB down -3.104 1.029e-19
Dscam1 down -1.795 1.792e-19
CG42534 down -4.148 4.16e-19
CG6125 down -2.153 7.197e-19
CG1688 down -3.061 8.789e-19
btv down -4.624 1.002e-18
Sb down -4.59 1.126e-18
CG43980 down -4.82 1.34e-18
Muc14A down -2.612 1.372e-18
hiw down -1.521 1.414e-18
CG3348 down -3.219 1.822e-18
Nos down -3.834 2.877e-18
CG30263 down -3.978 4.212e-18
jv down -2.334 4.212e-18
conv down -4.136 4.94e-18
NT1 down -6.652 4.94e-18
Dop1R1 down -2.643 6.474e-18
Shawl down -3.459 8.688e-18
CG8745 down -2.145 1.314e-17
CG14304 down -4.486 1.542e-17
CG31465 down -6.373 2.078e-17
Ugt86Di down -5.074 4.038e-17
CR44327 down -2.536 4.654e-17
salr down -3.028 4.671e-17
nompC down -3.89 6.068e-17
SIFaR down -4.022 6.357e-17
Nlg4 down -2.488 8.891e-17
CG15894 down -2.427 1.946e-16
Cda5 down -1.12 2.097e-16
CG4744 down -6.327 2.705e-16
eag down -1.729 2.931e-16
CG30272 down -3.39 3.009e-16
Ac78C down -2.352 3.672e-16
CG45105 down -3.336 4.007e-16
Rab26 down -2.214 4.049e-16
CG12950 down -2.918 4.628e-16
CG32791 down -1.702 5.419e-16
TkR99D down -3.825 8.6e-16
Ddr down -3.329 9.219e-16
GABA-B-R1 down -2.256 1.09e-15
Sytbeta down -3.292 1.449e-15
Hsp68 up 6.888 0
DnaJ-1 up 3.727 2.219e-143
Hsp70Bb up 7.003 2.219e-143
stv up 4.471 2.373e-104
Hsp26 up 4.279 5.676e-72
Hsp67Bc up 4.785 2.957e-71
Hsp27 up 3.532 4.06e-62
Hsp83 up 2.106 6.281e-58
Hsp23 up 6.872 8.789e-53
Nop17l up 1.614 7.563e-52
CG6770 up 1.78 5.402e-48
Hop up 1.305 1.268e-43
CG42240 up 1.131 1.65e-41
Hsc70Cb up 1.271 5.313e-38
Jafrac1 up 0.8308 7.251e-38
CG16721 up 1.484 1.699e-36
CG1416 up 1.24 1.833e-34
CG5290 up 1.882 8.359e-34
Droj2 up 1.165 9.102e-33
Hsc70-3 up 1.522 2.984e-32
Lsd-2 up 1.004 2.845e-30
alphagamma-element:CR32865 up 6.317 1.507e-29
sra up 1.258 9.836e-29
CG10600 up 1.189 1.267e-28
Mlf up 1.019 1.689e-28
Capr up 0.9256 6.875e-28
mim up 1.18 1.125e-26
Hsp70Bc up 5.778 5.299e-26
CG10077 up 1.398 5.714e-26
Pgi up 0.9688 3e-25
ref(2)P up 1.398 7.851e-24
CG7033 up 1.009 4.144e-23
e(y)3 up 0.9014 8.199e-23
Trxr-1 up 1.139 1.335e-22
Pa1 up 1.987 1.445e-22
CG1943 up 1.14 1.445e-22
PEK up 1.254 5.637e-22
GstD1 up 0.8593 7.088e-22
phol up 1.028 8.707e-22
CG3680 up 0.8435 4.633e-21
TfIIEalpha up 1.076 1.121e-20
da up 0.8578 2.725e-20
cact up 0.8173 3.294e-20
Ran up 0.7748 6.905e-20
CG1677 up 0.8251 9.427e-20
betaTub56D up 1.038 1.749e-19
Cctgamma up 0.8277 6.345e-19
BRWD3 up 0.8852 7.197e-19
l(1)G0469 up 1.272 7.197e-19
Pdk up 1.35 1.224e-18

2.2 Cold shock

gene cold_fc log2FoldChange.cold padj.cold
stan down -2.535 2.296e-20
Dhc93AB down -3.204 2.253e-19
CG3339 down -4.294 5.99e-19
CG1801 down -3.666 5.99e-19
CG3280 down -3.068 5.99e-19
CG42534 down -4.469 7.335e-19
CG32791 down -1.855 1.687e-17
ft down -2.987 8.646e-17
pip down -2.89 1.435e-16
Dscam1 down -1.683 2.136e-16
CG43163 down -3.52 4.912e-16
CG9492 down -3.725 5.06e-16
rk down -3.238 8.245e-16
Dhc36C down -2.296 1.463e-15
CG8219 down -5.491 1.463e-15
SIFaR down -4.039 2.331e-15
Ac78C down -2.361 3.608e-15
Ddr down -3.388 6.724e-15
d down -3.775 1.027e-14
CR45604 down -3.018 1.027e-14
mtt down -3.664 1.135e-14
Dhc62B down -3.892 1.49e-14
iav down -4.075 1.696e-14
CR45272 down -4.647 2.839e-14
prom down -2.737 2.839e-14
CG18519 down -3.233 2.839e-14
CG43110 down -3.216 4.113e-14
Nep5 down -3.804 4.113e-14
conv down -3.69 6.626e-14
rdgC down -1.94 6.946e-14
Shawl down -3.097 7.672e-14
CG44153 down -3.691 8.047e-14
Hsp68 down -1.071 8.344e-14
GluRIB down -2.415 9.254e-14
CG45002 down -1.938 9.254e-14
Sb down -3.89 1.557e-13
Nlg4 down -2.28 1.557e-13
CG4744 down -5.989 1.789e-13
trh down -2.138 2.011e-13
btv down -3.901 2.345e-13
rdo down -3.167 2.827e-13
Dop1R1 down -2.284 4.304e-13
unc-13-4A down -2.109 4.464e-13
TrpA1 down -4.111 4.79e-13
CG42255 down -1.631 5.093e-13
CG31814 down -3.185 5.781e-13
rad down -1.922 6.059e-13
Muc68Ca down -3.064 6.059e-13
CG43795 down -2.427 6.591e-13
eag down -1.562 7.105e-13
Jafrac1 up 0.6228 1.102e-19
Lsd-2 up 0.8045 1.486e-18
endos up 0.7605 1.544e-17
D1 up 0.684 1.687e-17
Muc4B up 2.542 1.687e-17
Capr up 0.7236 2.497e-16
CG14478 up 0.8465 3.717e-15
CG1677 up 0.73 7.404e-15
Ran up 0.6814 7.51e-15
CG15771 up 0.6845 1.537e-14
bif up 0.7919 2.869e-14
GstD1 up 0.7024 3.842e-14
e(y)3 up 0.7182 4.174e-14
mts up 0.638 6.428e-14
phol up 0.8291 9.254e-14
east up 0.7952 1.511e-13
Act5C up 0.6184 2.345e-13
CG8223 up 0.9441 2.752e-13
cact up 0.6657 4.446e-13
Rip11 up 0.7142 5.651e-13
CG1440 up 0.6414 5.951e-13
ssx up 0.6681 7.105e-13
swa up 0.8273 1.017e-12
tral up 0.8757 1.203e-12
CG1943 up 0.8542 1.883e-12
Pen up 0.898 2.887e-12
cib up 0.8765 3.891e-12
nocte up 0.7272 5.576e-12
CG6597 up 0.6554 5.593e-12
CG8963 up 0.6505 5.707e-12
mim up 0.7948 6.11e-12
Hmt4-20 up 0.7751 6.589e-12
CG12262 up 0.8364 1.29e-11
26-29-p up 0.8999 1.457e-11
rngo up 0.6756 1.476e-11
Jupiter up 0.6516 1.526e-11
CG4511 up 0.7374 1.68e-11
da up 0.6498 1.814e-11
pr-set7 up 0.8255 2.345e-11
Cap up 0.775 2.683e-11
CG10492 up 0.844 2.975e-11
Gapdh2 up 0.7177 3.343e-11
Rpt1 up 0.5432 3.942e-11
Df31 up 0.7823 4.048e-11
CG8108 up 0.6396 4.688e-11
betaTub56D up 0.7807 5.6e-11
Upf1 up 0.6236 5.655e-11
CG9705 up 0.7375 8.723e-11
Abi up 0.6488 8.733e-11
Amun up 0.7009 9.284e-11

3 Shared and unique - LFC scatter

3.1 No labels

3.2 GWAS hits labeled

3.3 With unique labeled

3.4 With shared labeled

3.5 With shared labeled (padj.hot)

3.6 With density plots

The ultimate goal is to have the density reflect the location of the GWAS hits for CTmin & CTmax

To be fixed soon…

4 GWAS

4.1 CTmax

4.1.1 All hits (pval cutoff 10^-5)

ID gene grps AvgEff AvgMixedPval
2R_10330800_INS Oaz INTRON 0.2164 8.00e-07
2R_6398772_SNP lola INTRON 0.3719 9.00e-07
2R_6398743_SNP lola INTRON 0.3710 9.00e-07
2R_10330805_SNP Oaz INTRON 0.2332 1.00e-06
3R_22515826_SNP 0.1838 2.30e-06
2L_12384183_SNP bru-2 INTRON 0.1670 2.40e-06
3R_25373467_SNP 0.3578 2.50e-06
2R_17564376_SNP CG30263 SYNONYMOUS_CODING 0.1794 2.60e-06
2R_10330722_SNP Oaz INTRON 0.2064 3.00e-06
X_3381582_SNP CG10803 INTRON 0.1864 3.20e-06
X_3381590_SNP CG10803 INTRON 0.1864 3.20e-06
2R_10330717_SNP Oaz INTRON 0.2102 3.50e-06
X_3381391_SNP CG10803 INTRON 0.1804 3.70e-06
X_3381587_SNP CG10803 INTRON 0.1849 4.10e-06
3L_9575326_SNP CG42673 INTRON 0.2063 6.00e-06
X_5876026_SNP Grip INTRON -0.1524 6.00e-06
3R_3427376_SNP CG34127 INTRON 0.1614 7.60e-06
2L_19428598_SNP CG16771 NON_SYNONYMOUS_CODING 0.1940 8.40e-06
2R_10330701_SNP Oaz INTRON 0.2015 9.70e-06
2L_19428336_SNP CG16771 SYNONYMOUS_CODING 0.2192 9.90e-06
3R_20025347_SNP twin INTRON 0.1599 1.00e-05
3L_14419091_SNP bbg INTRON -0.1660 1.03e-05
3L_1853643_SNP CG13936 INTRON -0.1620 1.42e-05
3R_18941021_SNP Rassf INTRON 0.1441 2.59e-05
2R_2894462_SNP Tsp42Ec INTRON 0.1546 2.92e-05
3L_1853640_SNP CG13936 INTRON -0.1510 3.62e-05
3R_7950242_SNP CG4702 INTRON 0.1614 3.67e-05
3R_23411999_SNP raps UTR_3_PRIME 0.3155 4.13e-05
X_15304333_SNP cngl INTRON 0.3127 4.89e-05

4.1.2 Group count

grps n
INTRON 23
SYNONYMOUS_CODING 2
NON_SYNONYMOUS_CODING 1
UTR_3_PRIME 1

4.1.3 Gene count (>2)

gene n
Oaz 5
CG10803 4
CG13936 2
CG16771 2
lola 2

4.2 CTmin

4.2.1 All hits (pval cutoff 10^-5)

ID gene grps AvgEff AvgMixedPval
2R_20313579_SNP prom INTRON 0.7260 0.00e+00
X_4385442_SNP CG32773 INTRON 1.0300 1.00e-07
3R_13900959_SNP 0.6348 2.00e-07
2R_20308502_SNP prom INTRON 0.6173 4.00e-07
3R_12992895_SNP Mur89F INTRON -0.6868 7.00e-07
2R_20313917_SNP prom INTRON 0.6276 9.00e-07
2R_20313922_DEL prom INTRON 0.6276 9.00e-07
2R_20313930_SNP prom INTRON 0.6276 9.00e-07
2R_20313933_SNP prom INTRON 0.6276 9.00e-07
2R_20313935_INS prom INTRON 0.6276 9.00e-07
2R_20313938_SNP prom INTRON 0.6276 9.00e-07
2R_20313940_MNP prom INTRON 0.6276 9.00e-07
2R_20308558_SNP prom INTRON 0.6119 1.00e-06
2R_20250118_SNP bs INTRON 0.5472 1.00e-06
2R_20301097_SNP CG3419 SYNONYMOUS_CODING 0.5562 1.10e-06
2R_20301239_SNP CG3419 NON_SYNONYMOUS_CODING 0.5434 1.10e-06
2R_20308533_SNP prom INTRON 0.5994 1.20e-06
2R_20313914_SNP prom INTRON 0.6215 1.30e-06
2L_2612712_SNP -0.7705 1.40e-06
2R_20313927_SNP prom INTRON 0.6177 1.50e-06
2R_20313911_SNP prom INTRON 0.6056 1.80e-06
2R_20307893_SNP prom NON_SYNONYMOUS_CODING 0.5823 1.80e-06
2R_20313916_SNP prom INTRON 0.6222 1.90e-06
2R_20308565_SNP prom INTRON 0.6001 1.90e-06
2R_20309964_SNP prom INTRON 0.6214 2.00e-06
2R_20309106_SNP prom INTRON 0.5709 2.20e-06
3R_11364111_SNP CG18519 SYNONYMOUS_CODING 0.6916 2.20e-06
2R_20313919_SNP prom INTRON 0.6250 2.40e-06
3R_14850882_SNP CG14285 NON_SYNONYMOUS_CODING 0.7111 3.10e-06
2R_20313912_SNP prom INTRON 0.6180 3.20e-06
2L_3465546_SNP msl-2 NON_SYNONYMOUS_CODING 0.9493 3.20e-06
2R_20301123_SNP CG3419 NON_SYNONYMOUS_CODING 0.5247 3.30e-06
3R_13552400_SNP Lgr1 INTRON -0.9664 3.60e-06
3R_11367299_SNP CG18519 NON_SYNONYMOUS_CODING 0.7277 4.00e-06
3R_11288771_SNP CG14869 INTRON 0.9176 4.20e-06
2R_20301091_SNP CG3419 SYNONYMOUS_CODING 0.5258 4.20e-06
2R_12301745_SNP Sema-2b INTRON -0.5963 4.20e-06
3R_12990694_SNP Mur89F INTRON 0.5249 4.30e-06
2R_20309307_SNP prom INTRON 0.5642 4.80e-06
3R_9949217_SNP twf SYNONYMOUS_CODING 0.7970 5.60e-06
3R_13002842_SNP Mur89F INTRON 0.5265 5.70e-06
2R_20309122_SNP prom INTRON 0.5473 5.80e-06
3R_12997215_SNP Mur89F INTRON 0.5159 6.00e-06
2L_3396579_SNP 0.9004 6.60e-06
2L_3396577_SNP 0.8995 6.70e-06
3R_13552010_SNP Lgr1 INTRON -1.0970 6.70e-06
3L_4694662_SNP CG15876 SYNONYMOUS_CODING -0.5194 7.50e-06
X_5639729_SNP IntS6 INTRON 0.8784 7.50e-06
2L_2612282_INS CG15395 DOWNSTREAM -0.7986 7.60e-06
2R_7024700_SNP BBS4 SYNONYMOUS_CODING 0.8879 7.80e-06
2R_20313809_SNP prom INTRON 0.5613 9.00e-06
3L_5853164_SNP 0.5565 9.60e-06
2L_3885863_SNP capu INTRON 0.4909 9.70e-06
2R_20263633_SNP bs UTR_3_PRIME 0.5679 1.07e-05
3L_8696154_SNP 0.8089 1.07e-05
2R_20308557_SNP prom INTRON 0.5645 1.08e-05
2R_20313929_SNP prom INTRON 0.5872 1.11e-05
3R_11388164_SNP 0.5080 1.22e-05
2R_15691303_SNP -0.8674 1.23e-05
2R_20314643_SNP prom INTRON 0.5688 1.26e-05
3L_14188075_SNP nuf INTRON 0.5235 1.30e-05
2R_20250001_SNP bs INTRON 0.5296 1.37e-05
2R_10963282_SNP 0.5813 1.40e-05
3R_5901971_SNP CG5361 UPSTREAM -0.9199 1.48e-05
2R_20308551_SNP prom INTRON 0.5059 1.51e-05
2R_20306042_SNP prom INTRON 0.4978 1.52e-05
2R_17037739_INS CG30389 INTRON 0.9023 1.55e-05
X_6270410_SNP 0.6623 1.55e-05
3R_12992188_SNP Mur89F INTRON 0.4925 1.61e-05
2R_20280640_SNP slik DOWNSTREAM 0.5158 1.81e-05
X_14991195_SNP rab3-GEF INTRON 0.4949 1.83e-05
3R_12997318_SNP Mur89F INTRON 0.4879 2.01e-05
2R_20263506_SNP bs NON_SYNONYMOUS_CODING 0.5286 2.02e-05
2R_20263738_SNP bs UTR_3_PRIME 0.5286 2.02e-05
2R_20263740_INS bs UTR_3_PRIME 0.5286 2.02e-05
2R_20263742_SNP bs UTR_3_PRIME 0.5286 2.02e-05
2R_3772050_SNP Dgk INTRON 0.5197 2.10e-05
2R_20313932_SNP prom INTRON 0.5951 2.19e-05
2R_20257701_SNP bs INTRON 0.5248 2.30e-05
2R_20252998_SNP bs INTRON 0.5041 2.36e-05
2L_16629322_SNP CG42389 INTRON -0.4818 2.42e-05
2R_20280846_SNP slik DOWNSTREAM 0.5190 2.43e-05
X_5908964_SNP 1.0450 2.58e-05
2R_20257613_SNP bs INTRON 0.5202 2.70e-05
3R_5905483_SNP -1.0390 2.70e-05
3R_4247244_SNP CG43462 INTRON -0.5526 2.83e-05
3R_9755188_SNP -0.5000 2.85e-05
2L_1964167_SNP erm INTRON -0.6578 2.87e-05
2R_20280809_SNP slik DOWNSTREAM 0.5103 2.96e-05
X_7604829_INS 1.0340 3.04e-05
2R_20260408_SNP bs INTRON 0.5402 3.32e-05
2R_12696827_SNP 0.5654 3.35e-05
2R_14565483_DEL CG15086 DOWNSTREAM -1.0320 3.45e-05
2R_1991490_SNP EcR INTRON 0.9278 3.60e-05
2R_1991491_SNP EcR INTRON 0.9278 3.60e-05
2L_1090401_SNP CG4629 INTRON -0.9396 3.60e-05
2R_17983519_SNP CG11073 INTRON 0.4746 3.78e-05
3L_3812775_SNP CG12006 SYNONYMOUS_CODING -0.4898 3.86e-05
2R_20258747_SNP bs INTRON 0.5115 4.07e-05
3L_3812970_SNP CG12006 SYNONYMOUS_CODING -0.6748 4.94e-05

4.2.2 Group count

grps n
INTRON 60
SYNONYMOUS_CODING 8
NON_SYNONYMOUS_CODING 7
DOWNSTREAM 5
UTR_3_PRIME 4
UPSTREAM 1

4.2.3 Gene count (>2)

gene n
prom 30
bs 12
Mur89F 6
CG3419 4
slik 3
CG12006 2
CG18519 2
EcR 2
Lgr1 2

5 DEG & GWAS

5.1 Expression Plots

Cold vs Ctrl

Hot vs Ctrl

5.2 CTmax & DEG Corr

5.3 CTmin & DEG Corr